Post Iron Man 3
by LokiLove24028
Summary: Pepper is infected with extremis, Tony's suits are all destroyed, the house is gone, and Happy is still in a coma. Set after the events of Iron Man 3 about what Pepper and Tony do to cope with their new losses and where they go from there.
1. Chapter 1: Clean Slate Protocol

"The clean slate protocol, sir?" Jarvis asked through his ear piece. Pepper stared back at him with the same confused look on her face when she caught him doing something out of the ordinary. Tony looked back at her and her ruffled hair with make-up under her eyes. The truth that he wasn't able to protect her was still unbearable for him. They hurt her, and he couldn't do anything. It made Tony feel sick to his stomach, but it was all over now… almost.

"Screw it, it's Christmas. Yes… yes." Tony answered his AI, nodding on each yes. As he said this he slowly moved forward towards Pepper to wrap both of his arms around her back. He could tell that she was both confused and still frightened about what had happened only moments ago. He couldn't do anything but hold her for that moment though. She hesitantly wrapped an arm behind his shoulders, leaving the arm with the ironman armor at his side.

Over Pepper's shoulder, Tony could see the numbers of suits flying around in the sky above them in aimless circles. He knew he was seeing for the last time when he heard the first explosion behind him. Stark watched as the parts of the boat reflected the light from the explosion as sparks rained down above them. The clean slate protocol was now in effect, and the first ironman suit was destroyed.

It wasn't long before the next explosion sounded from somewhere long off from his right shoulder. Tony watched the next suit explode in midair as more sparks flew like fireworks in the dark Christmas night sky. They began to go faster now, one boom after another as the suits were destroyed in midflight one by one.

Pepper let out a surprised breath over his shoulder as she watched the suits go, her hair brushing up against Tony's face as she looked back and forth. Tony was reluctant to watch Jarvis blow up his suits. He'd spent countless hours on all of those, all the way up to Mark 42. He realized that that was the reason he was destroying them though. They were only a distraction, an obsession, to keep him away from Pepper and the ones he loved. He had submerged himself in his work instead of being the person he should be for his Pepper.

Pep's grip tightened around his shoulders. Tony turned and pressed his lips against the side of her forehead, pulling her close. He took a deep breath, taking in the smell of her hair that he had missed so much. He kissed her and turned back to look over her shoulder.

"Okay so far? You like it?" Tony asked, glanced over at Pepper. He heard Pepper give a happy sigh.

"It'll do." she said, making him smile. She tightened her grip on him even more. They hugged for a while like that, the last of the suits exploding around them. Finally, the sounds of the suits being blown up decreased into nothing which was when Tony stepped back to look at Pepper. She was worn, but she was still his Pepper. He gave a half smile to her making her smile back.

"What?" she asked.

"Nothing. I just missed you that's all." Tony commented. He noted the ironman arm still enclosed around hers as well as her black sports bra which was the only thing she was wearing as far as above waist level.

"Let's get that armor off of you." Tony said. He reached for Pepper's arm which she extended towards him. He turned it so her hand was palm up. The red painted armor gleamed in the lights that were stranded around parts of the ship. As she reached her arm out, the familiar mechanical whine that the armor made while it moved filled Tony's ears. He realized it would be the last time he heard that sound from the armor for a while.

Wiping the thought out of his head, Tony reached for the small latch at the joint of the arm armor and flipped it up. The pieces of the suit retracted from each other and clanked to the ground in a pile of parts. Pepper rubbed her arm where the armor used to be clad. Tony took this time to take off the jacket he was wearing. One of the sleeves was completely ripped off while the other was still attached, but it was probably the most intact thing on his body.

Tony wrapped the jacket around Pepper's back and helped her get her arms through the sleeves. It was much too big for her, making Pepper look even smaller. It was better than just being in her sports bra however.

"Thanks…" she mumbled as she zipped it up. Tony waited until she fastened the jacket around her before he enclosed her in his arms again. She wound her own arms around his neck and nestled her head in the spot where his neck met his shoulder. Pepper's warm breathing down his neck made Tony slightly shiver as he buried himself in her hair. Pep smirked at this before pulling away to look up at Tony.

"Hey!" Tony heard a voice come from behind Pepper. He looked over her shoulder to see Rhodey running to them still wearing the Iron Patriot armor. The mask was flipped up so Tony could see his friends face as he ran towards them. "Everyone alright?" Rhodey asked.

"For now." Tony said. Pepper turned to face Rhodey, allowing Tony to wrap his hands around her waist from behind.

"Nice to see you Pepper." Rhodey said giving her a slight nod.

"You too Rhodes." she replied. Tony kissed the top of her head before remembering something.

"Rhodey, where's the president?"

"Ah, the ambulances and police force showed up at the docks." Rhodey said. He added a slight eye roll. "Finally." He murmured. "He's getting checked out so they can be sure he's alright, I suggest you two do the same."

"Nooooooooooo…" Tony complained. Pepper twisted around a bit to look at him with an irritated look. "What?" he asked her. "You know I hate hospitals, and ambulances, and people being in control of my wellbeing. It's unsettling."

"You aren't the qualified one here!" she said. Tony rolled his eyes.

"Who needs qualification anymore." he retorted. He knew there was no winning this argument however.

"Will you quit whining for once and take two seconds to make sure you aren't dying?" Rhodey asked. Pepper had already taken Tony by the hand and had begun dragging him towards the mainland anyway. He followed her but dreading what was coming next. There were undoubtedly tons of reporters waiting once they got off the boat. The idea would have excited him a couple months back, but it was going to be hell going through it now. He was "back from the dead" even though he never was in the first place. He had no home to go back to, he had no workshop to relax and tinker in, no dummy or butterfingers to boss around. The realization sent a pang of depression through Tony's body. It was suddenly gone when he watched Pepper walking in front of him, pulling Tony along by the hand. He had her, and that was all that mattered.

~X~

The bright lights flashed all around him. The annoying clicks of the cameras filled the air and the roar of shouting reporters erupted into the night.

"Tony Stark! Tony Stark!"

"Where have you been since you house was destroyed?"

"Did you defeat the Mandarin?"

"Who exactly is the Mandarin?"

"Were you aware that Miss Potts was involved?"

"How did you survive the destruction of your mansion?"

"What will you do next?"

The reporters were gathered on every side around the ambulance. Officers held them back to the best of their ability, but they were still way too close than Tony wanted them. Their questions were all meaningless statements to him that he wouldn't answer. He tried to block out the noise while the nurses and doctors from the ambulance checked him, but the last question hit him. What would he do next?

Tony felt Pepper hand slip into his as she laced their fingers together. She squeezed his hand knowing full well that the reporters were probably getting to him. He looked over at her with sad eyes that made her frown.

"Where do we go next?" Tony asked as quiet as he could while still being able to be heard over the nagging paparazzi. Pepper looked up at him with wide eyes. The nurse on the other side of her was gently prodding her shoulder and patching it up with bandages.

"I- I don't know." she answered. "I mean… we could go stay at the Tower for a while."

As soon as these words came out of Pepper's mouth, Tony felt a constricting feeling in his chest. It kept getting tighter and tighter, gripping his heard and twisting it in knots. Tony's breathing became labored as it became harder to actually get breaths. He looked away from Pepper and stared at a spot on the ground. _Focus, focus. You'll be okay. You'll be okay. _Tony tried to tell himself. It was no use though. The anxiety attack took hold of him and he could keep control any longer.

Breaking away from Pepper's grip on his hand, he quickly walked forwards and into the crowd of reporters. He had no idea where he was going but everything was getting blurry. The shouts and yells became even louder around him as the journalists and paparazzi buzzed around him. There were so many flashes of bright light that Tony could see where he was going. He felt the shoves of people around him and the distant call of his name from Pepper somewhere behind him. He only kept walking though as the world began to spin and become more and more blurry. Tony was breathing extremely fast now and broke into a jog.

Finally, he broke from the crowd. They formed a cloud of people behind him pointing microphones and cameras, but Tony just kept running. He could make out a spinning brick building, the stretching parking lot and the street lights that surrounded him, but he hardly paid attention. He reached the brick wall right before he collapsed against it. Tony tried to regain the strength in his legs but it was too difficult. He eventually gave in and slid to the ground, pressing his back against the wall and pulling his knees to his chest. Tony could clearly hear his loud breathing through the night. He tried to calm it down but he just couldn't think straight.

"Tony!" he heard Peppers voice. He didn't look for her though; he could only focus on breathing. "Tony…" he heard her soft voice come up beside him. He was still breathing in fast loud, short breaths while tightly gripping his knees. Pepper knelt in front of him but still gave him a considerable amount of room. She reached forward to take his hand.

"Shhh… breathe… Just breathe, Tony." she said soothingly. He heard her words and tried to focus but he couldn't, he couldn't… "I'm here, Tony." Pepper said quietly but in a firm way that was comforting. Tony finally raised his eyes to look into hers. She looked frightened despite her calm words. He didn't mean to frighten her; he just couldn't control the anxiety attacks sometimes.

While lost in Pepper's eyes, Tony barely noticed his breathing calming down to a normal pace. The word became more clarified and less blurry and his head stopped spinning. A sense of relaxation and comfort washed over him knowing that Pepper was there. Tony finally took a deep breath and closed his eyes. He let his head gently fall back against the brick wall as he caught the rest of his breath.

"What the hell was that all about?" Pepper breathed. She moved to sit down beside him, keeping her hand in his. Tony opened one eye to glance at her before closing it again.

"I- I might have a slight of an anxiety issue." he said. Before Tony could continue Pepper immediately spoke up.

"An anxiety issue!?" she demanded. "And you didn't bother to tell me?"

With this, Tony opened his eyes and turned to look at her. Their faces were less than 6 inches away from each other as Tony tried to explain.

"No, no… I just found out not too long before the house was attacked. I was at a restaurant with Rhodey and these kids wanted me to sign some picture about New York and I flipped out. It's happened about two other times with mentions of the Avengers. I- I try to make it stop but-"

"Tony, it's ok. It isn't something that's easy to control. It will take time." Pepper said.

"There are aliens… _aliens_, Pepper. What the hell is that about? We don't even know if they're coming back or how many there are or how many are set on destroying Earth or…"

"Well Thor doesn't seem so bad. He's definitely not from Earth." Pepper pointed out. Tony raised his eyebrows. He supposed she was right. The thought of Thor made him smile.

"Point-break…" he whispered under his breath. "Yeah I guess Asgardians are okay."

"I'm sure everything will be okay." Pepper said. Tony nodded and they sat there in peace for a while. It was then when Tony realized that it was a pretty nice night. The stars were scattered throughout the sky and there was a warm breeze that blew past him once and a while. He squeezed Pepper's hand, grateful to be able to be there with her. After near death experiences with both of them in the course of a few days, he found himself once again appreciating everything more.

"Why don't we get a hotel room tonight and see how you feel about New York in the morning." Pepper said pausing a bit as she hesitantly said New York. Tony nodded and pushed himself off the ground, offering a hand to Pepper. She took it and stood.

"Let's get out of here." Tony said looking over at the mob of reporters.

"What about telling Rhodey?" Pepper asked.

"Rhodey can wait, I'm exhausted."


	2. Chapter 2: Miami Hotel

Tony opened the door to the room and guided Pepper inside. She had fallen asleep in the taxi on the way there and was barely awake now. She heavily leaned into Tony's side. He closed the door behind them with one arm as he kept the other around her. As he flipped the lights on, she groaned.

"It's ok baby, we'll go to sleep soon." Tony murmured to her. This made her perk up.

"Wait, but I want to take a shower first there's no way I'm going to bed like this." she said as if all exhaustion was gone. Tony smirked and nodded.

"Ok, ok." he said. "Am I not invited this time?" he asked. Pepper turned to him and gently ran her fingers under his eye where there was a deep cut with bruising around it.

"Too much blood I don't want you to get worried over." Pepper said. "And… I- I don't want to… to…" Pepper faded off as her gaze shifted from Tony to somewhere far off. She frowned as her eyebrows came together.

"Pepper… Pepper, honey." Tony said taking each of her wrists in his hands. Her attention returned to his face with big eyes. She looked frightened, but he couldn't blame her. The extremis was running through her veins. It was the very same serum that was responsible for countless deaths, whether it be for the destruction caused by the person using extremis for killing or the extremis becoming unstable to the point of explosion. He had to get her the cure before that could happen.

"Pepper, you won't hurt me. I trust you. You can control it better than I ever could." Tony told her. She relaxed in his grip for a moment before falling against his chest. He wrapped his arms around her and rubbed her back to comfort her.

"Hurry up though; I want a shower after you." Tony told her. She pulled away and tiredly smiled at him.

"Alright I'll be quick."

~X~

Pepper heard the mumbled on the TV and the running shower from in the bathroom, but it was all distant noise to her. She suddenly let go of all thoughts as she drifted further under into sleep. The big comforter and soft pillows felt _soooo _good after spending who-know-how-long in a cold cement basement. She was safe, Tony was safe, Rhodey was safe, the president was safe… now the only thing she wanted to do was sleep. The shapes in the room blurred as the sounds became quieter in her mind. Soon after that, she fell into the darkness of sleep blocked out all sound and thought.

~X~

Tony opened the bathroom door wearing only boxers and the new pajama pants that they picked up at some all-night shop at the edge of Miami. All of their clothes were destroyed with the house except for the ones they kept at the tower in New York. Now that Tony thought about it, going back to stay at the tower was the reasonable thing to do. They had their only remaining stuff there and it was his only other house in the U.S that he could think of. Unless they suddenly wanted to move to the house in Dubai, New York was their best option.

Pepper was asleep already on the bed. The comforter slowly rose and fell with her steady breaths. Her hair spilled over her back and shoulder as she lied on her side, facing away from Tony. He took a moment just to watch her sleep. She was safe, and he couldn't be more grateful for anything but that. He may have lost his house, and cars, and suits, but watching Pepper made him realize he really didn't care as long as he had her. Tony had made a promise to himself to protect her, and then she got hurt. He was just lucky that she was still here with her.

Tony ran his hand through his wet hair before looking at the clock on the nightstand. It was already two seventeen in the morning on December 26th. It had been an interesting Christmas. They had been fighting extremis soldiers instead of sitting at home together while cuddling by the fire, but it would definitely be memorable, even if Tony didn't want to remember it. He had to admit however, he couldn't imagine a life without being Iron Man. He couldn't imagine not heading into battles with crazed people with dreams of making people with fire powers or electric whips or using his suit technology against him. The only word he could think of without all those things was _boring_. He was Iron Man now, everyone counted on him to protect them from the strange outlandish superhero stuff that others couldn't. Although he wished it didn't jeopardize his life as well as Pepper's so often, there was no way of going back now. He had to rebuild the suits soon, only a few though so they weren't a distraction. He'd make everything better.

With that in mind, Tony climbed into the bed next to Pepper. He pulled the comforter over himself and scooted closer to Pepper. He realized the TV was still on, so he reached over to the nightstand for the remote to turn it off. The room was a nice silence then, and suddenly the exhaustion wore in on him. He hadn't gotten more than five hours of sleep in 5 days or so. The fatigue finally hit him like a brick wall, no adrenaline to keep him going anymore. Tony turned off the light as he was already leaning over the nightstand. The hotel room was perfectly dark as he turned back to Pepper to press his bare chest against her back to wrap and arm around her waist. Pepper softly mumbled something in her sleep making Tony smile and hold her closer.

Tony laid his head on the pillow pulled up right next to her. He gently nuzzled the back of her neck. As he did so, he realized that Pepper was getting slightly warmer, her waist and neck. He opened his eyes to see a light glow spreading throughout her body. He quietly chuckled as her body temperature rose to a warm heat that wasn't very hot. He wondered what made her get warmer. Tony wanted to know so much about the extremis, and there was so much to learn. He knew that he shouldn't, however. He needed to get the serum out of Pepper as quickly as possible. Right now, she looked awfully cute as she barely glowed a warm heat that thankfully wasn't catching anything on fire. Tony nestled close to her once again before letting sleep consume him.

~X~

A breeze brushed over Tony's face and blew throughout the room. He scrunched up his nose at the contact before groggily opening his eyes. For a moment his heart skipped when Tony completely forgot where he was. There were only dark lumps and objects surrounding him with a sliver of light by a wall that look like a slightly opened glass door. As his eyes adjusted in the darkness, Tony could make out the features of the hotel room as he remembered the events of the night before. The sudden realization of all the action that had happened hit him, including the close call of Pepper's death.

Tony turned to the other side of the bed where he reached out for Pepper, but he only found empty sheets and pillows. Fear gripped his chest by the instinct of constantly being in danger in the last couple days, but he remembered that everything was now over and let his anxiety go. Tony recalled the slightly opened the door and finally put it together as he swung his legs over the edge of the bed sleepily. Looking at the clock, it was only four in the morning. He wondered why Pepper was up so early.

Tony walked out onto the balcony and immediately felt the warm breeze get stronger on his face, chest, and arms. Pepper was sitting up against the wall facing outwards towards the city of Miami past the balcony railings. She sat with her legs crisscrossed on the ground with her head bowed down. The familiar light red hair that Tony loved spilled over most of her face as she fidgeted with her hands in her lap. He didn't notice it at first, but he could see the slightest shake of her shoulders.

"Pep?" Tony said worried. He instantly rushed to sit next to her, sitting the same as she was. He put his right arm around her shoulders and held her hand in his left to stop her from fidgeted. She raised her head and let her hair fall from her face and across her shoulders. From the light of the moon and the lights of the buildings around them, Tony could tell that she had definitely been crying. He squeezed her shoulders and leaned his head into hers.

"What's wrong Pep?" he asked calmly. He raised his eyebrows at her as he angled his head to see her sadly smile.

"Nothing really… Everything that happened just started settling in." she said looking back down at her hand entwined in Tony's. Tony kissed the side of her head and held her closer. Pepper straightened and looked Tony in the eyes. Hers were red even in the dim lighting of the night, making her irises look even bluer.

"Tony, you nearly died. I thought you were dead." Pepper solemnly said. Tony gave her a sad smile before gently moving a piece of hair out of her face and leaving his hand at the back of her neck.

"I know… You did as well, and it was the scariest moment of my life." Tony said so low it was nearly a whisper. He gently pushed his forehead against hers and studied her face. _God, I love her. _Was all he could think. "We're okay now, babe." he reassured her.

When Pepper didn't say anything back, Tony leaned forward while gently pulling her closer by the back of her neck. His lips met hers as they kissed for the first time in a long while. It was a lot more than that though. It was their first kiss after nearly losing each other, after believing they lost each other. They had been through so many unimaginable things in only a couple of days, but they were finally together and safe again.

Tony pressed further into Pepper and farther into the kiss as they enjoyed their moment of peace on the balcony together. Tony felt Pepper wrap her arms tightly around his neck as she slowly laid down on her back, Tony following by moving right above her. Before they could get too far however, Pepper pulled away and looked up at Tony. She gazed into his eyes for a moment, making him shoot her a confused glance.

"You're exhausted, let's go to bed." Pepper said to him as she ran a hand through his hair.

"But…" Tony began to protest, but Pepper already wriggled her way out from under him.

"Come on, we can continue in the morning." Pepper said starting back inside.

"But it is the morning." Tony called after her. She looked back at him before entering the room as she rolled her eyes.

"Smart-ass." she mumbled, but she was smiling ever so slightly. Tony smiled and followed her in. He moved to the bed, lay down, and closed his eyes as he wait for Pepper to join him on the other side of the bed. He waited half a minute without feeling her get into bed next to him. He opened one eye to see Pepper grabbing a blanket and pillow to go lie on the couch by the door. Tony's heart dropped. Now what?

"Pep, whatcha doin?" he asked her. She didn't look at him but instead spread out the blanket on the couch.

"There's no way I'm going to trust myself to be that near you when I'm sleeping." she said seriously. Tony sighed.

"Haven't we been over this? You won't hurt me, Pepper." Tony said, trying to reassure her once again that she wouldn't burn him with her extremis. He wasn't just saying it to get her to sleep next to him either, he meant it.

"So you didn't notice?" Pepper asked. Tony frowned and watched her throw her pillow down at the head of the couch while still not looking up.

"What?" he asked. Tony rubbed his hand over his face. He just wished Pepper would come lie down with him for the first time in days.

"The pillowcase and middle blanket…" she said ever-so quietly. Tony shot a confused glance towards her that she didn't look over to see anyway. He twisted towards Pepper's side of the bed to turn the light on that sat on her nightstand. As soon as the room was illuminated again, he immediately saw what she meant.

The entire corner of the pillow that Pepper hadn't grabbed was charred and filled with burned holes. The top of the blanket Pep was talking about looked the same with blackened areas and missing areas. Tony's eyes went wide for a moment before his mood changed. He tried to suppress a laugh which turned into more of a choked chuckle as he bit his lip while trying not to smile. Pepper shot an angry glance towards him.

"It's not funny…" she said. "I could have hurt you!" Tony let himself smile as he examined the burned pillow and blanket.

"Pepper, I'm pretty sure I'd wake up before you burnt me to a crisp." Tony argued. Pepper just shook her head and dropped onto the couch. She fluffed her pillow and pulled the blanket over herself as she closed her eyes. Tony watched her before turning out the lights. He mimicked her actions with the pillow and blanket before pushing his head into his pillow while still watching her silhouette. There was no way he was going to stand for this.

"Brrr…" he said as he pretended to shiver. "It sureeeee is cold over here."

Pepper stirred but didn't look over at Tony. He rolled his eyes and wrapped his arms around himself as though he was cold.

"Sure wish I had someone to keep me warm…" he said not-so-subtly. "Sooooo coldddd!"

Tony heard Pepper sigh and waited for her to give in, but no such luck.

"Man, if only I had an extremis girlfriend that could keep me warm so I didn't have to suffer miserably over here. Someone who got all warm and glowy when I cuddled them-"

"Oh stop, I do not do that." Pepper finally spoke up. Tony smiled. He knew that he had her.

"Oh yes you do. When I got into bed and cuddled you, you began to glow and get all warm." Tony said smiling, remembering how she had done that in her sleep. "It's adorable."

"Is not, it's annoying." Pepper countered.

"Soooo colddd!" Tonys said once again. Pepper let out a loud annoyed side before throwing the blanket off her and standing up. She picked up her pillow and carried it to the bed where she threw it down next to Tony's head.

"Are you happy now?" she asked as she climbed in next to him. Tony gave her a smug smile before scooting closer to her to protectively wrap an arm around her waist once again.

"Very happy." he said.


End file.
